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PRPF31 pre-mRNA processing factor 31 [ Homo sapiens (human) ]

Gene ID: 26121, updated on 11-Apr-2024

Summary

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Official Symbol
PRPF31provided by HGNC
Official Full Name
pre-mRNA processing factor 31provided by HGNC
Primary source
HGNC:HGNC:15446
See related
Ensembl:ENSG00000105618 MIM:606419; AllianceGenome:HGNC:15446
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RP11; PRP31; SNRNP61; NY-BR-99
Summary
This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]
Expression
Ubiquitous expression in spleen (RPKM 14.1), endometrium (RPKM 14.0) and 25 other tissues See more
Orthologs
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Genomic context

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See PRPF31 in Genome Data Viewer
Location:
19q13.42
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54115754..54131713)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57194406..57210410)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54619134..54635144)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene osteoclast associated Ig-like receptor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54605952-54606928 Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54617323-54618196 Neighboring gene TCF3 fusion partner Neighboring gene PRPF31 antisense RNA 1 Neighboring gene CCR4-NOT transcription complex subunit 3 Neighboring gene uncharacterized LOC102724273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54662792-54663461 Neighboring gene leukocyte receptor cluster member 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus. Chen Z, et al. Hum Mutat, 2022 Dec. PMID 36317469
  2. Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up. Lisbjerg K, et al. Ophthalmic Genet, 2023 Apr. PMID 36164253
  3. Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells. Georgiou M, et al. Clin Transl Med, 2022 Mar. PMID 35297555, Free PMC Article
  4. Clinical Evidence for the Importance of the Wild-Type PRPF31 Allele in the Phenotypic Expression of RP11. Roshandel D, et al. Genes (Basel), 2021 Jun 14. PMID 34198599, Free PMC Article
  5. Heterozygous deletions of noncoding parts of the PRPF31 gene cause retinitis pigmentosa via reduced gene expression. Ruberto FP, et al. Mol Vis, 2021. PMID 33907366, Free PMC Article

See all (238) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Precision Therapy Approach for Retinitis Pigmentosa 11 Using Splice-Switching Antisense Oligonucleotides to Restore the Open Reading Frame of PRPF31.
    Title: A Precision Therapy Approach for Retinitis Pigmentosa 11 Using Splice-Switching Antisense Oligonucleotides to Restore the Open Reading Frame of PRPF31.
  2. Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome.
    Title: Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome.
  3. Long Noncoding RNA RP11-89K21.1 Interacts with miR-146a/b-5p to Promote Proliferation and Gefitinib Resistance Through Regulating RHPN2 and RhoA/ROCK Pathway in Lung Adenocarcinoma.
    Title: Long Noncoding RNA RP11-89K21.1 Interacts with miR-146a/b-5p to Promote Proliferation and Gefitinib Resistance Through Regulating RHPN2 and RhoA/ROCK Pathway in Lung Adenocarcinoma.
  4. Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up.
    Title: Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up.
  5. Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus.
    Title: Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus.
  6. PRPF31 interacts with PRPH2 confirmed by co-immunoprecipitation and co-localization.
    Title: PRPF31 interacts with PRPH2 confirmed by co-immunoprecipitation and co-localization.
  7. LncRNA RP11805J14.5 functions as a ceRNA to regulate CCND2 by sponging miR34b3p and miR1395p in lung adenocarcinoma.
    Title: LncRNA RP11‑805J14.5 functions as a ceRNA to regulate CCND2 by sponging miR‑34b‑3p and miR‑139‑5p in lung adenocarcinoma.
  8. Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells.
    Title: Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells.
  9. Determinants of Disease Penetrance in PRPF31-Associated Retinopathy.
    Title: Determinants of Disease Penetrance in PRPF31-Associated Retinopathy.
  10. Molecular genetics of inherited retinal degenerations in Icelandic patients.
    Title: Molecular genetics of inherited retinal degenerations in Icelandic patients.
Submit: New GeneRIF Correction See all GeneRIFs (84)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Retinitis pigmentosa 11
MedGen: C1838601 OMIM: 600138 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, pre-mRNA processing factor 31 homolog (PRPF31), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp566J153

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables U4 snRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables U4atac snRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-macromolecule adaptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ribonucleoprotein complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables snRNP binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
acts_upstream_of_or_within mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in ribonucleoprotein complex localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
NOT involved_in snoRNA localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within spliceosomal tri-snRNP complex assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spliceosomal tri-snRNP complex assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spliceosomal tri-snRNP complex assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Cajal body IDA
Inferred from Direct Assay
more info
 PubMed 
part_of MLL1 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IC
Inferred by Curator
more info
 PubMed 
part_of U4 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U4 snRNP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of U4atac snRNP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4atac snRNP TAS
Traceable Author Statement
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of spliceosomal tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
U4/U6 small nuclear ribonucleoprotein Prp31
Names
PRP31 pre-mRNA processing factor 31 homolog
U4/U6 snRNP 61 kDa protein
hPrp31
protein 61K
serologically defined breast cancer antigen NY-BR-99

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009759.2 RefSeqGene

    Range
    5002..20961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_015629.4 → NP_056444.3  U4/U6 small nuclear ribonucleoprotein Prp31

    See identical proteins and their annotated locations for NP_056444.3

    Status: REVIEWED

    Source sequence(s)
    BC117389, CB854773
    Consensus CDS
    CCDS12879.1
    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439
    UniProtKB/TrEMBL
    E7EVX8
    Related
    ENSP00000324122.4, ENST00000321030.9
    Conserved Domains (2) summary
    pfam01798
    Location:100 → 330
    Nop; snoRNA binding domain, fibrillarin
    pfam09785
    Location:337 → 465
    Prp31_C; Prp31 C terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    54115754..54131713
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006723137.5 → XP_006723200.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    See identical proteins and their annotated locations for XP_006723200.1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439
    UniProtKB/TrEMBL
    E7EVX8
    Conserved Domains (2) summary
    pfam01798
    Location:100 → 330
    Nop; snoRNA binding domain, fibrillarin
    pfam09785
    Location:337 → 465
    Prp31_C; Prp31 C terminal domain

  2. XM_047438587.1 → XP_047294543.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    Related
    ENSP00000395894.1, ENST00000445811.5

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    90247..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329672.1 → XP_054185647.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

  2. XM_054329673.1 → XP_054185648.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X3

  3. XM_054329674.1 → XP_054185649.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    90202..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330157.1 → XP_054186132.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

  2. XM_054330156.1 → XP_054186131.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NW_003571056.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    90247..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330464.1 → XP_054186439.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

  2. XM_054330465.1 → XP_054186440.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NW_003571057.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    90202..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330718.1 → XP_054186693.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

  2. XM_054330717.1 → XP_054186692.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NW_003571058.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    90247..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330948.1 → XP_054186923.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

  2. XM_054330949.1 → XP_054186924.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NW_003571059.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    90247..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331226.1 → XP_054187201.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

  2. XM_054331227.1 → XP_054187202.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    90202..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331502.1 → XP_054187477.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

  2. XM_054331501.1 → XP_054187476.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

Reference GRCh38.p14 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

    Range
    90247..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333537.1 → XP_054189512.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

  2. XM_054333538.1 → XP_054189513.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X4

  3. XM_054333539.1 → XP_054189514.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

    Range
    90247..106257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333639.1 → XP_054189614.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

  2. XM_054333640.1 → XP_054189615.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    57194406..57210410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320498.1 → XP_054176473.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

  2. XM_054320497.1 → XP_054176472.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

    UniProtKB/Swiss-Prot
    E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WWY3.2 GenPept UniProtKB/Swiss-Prot:Q8WWY3

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